Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 183 bits (465), Expect = 6e-51 Identities = 119/359 (33%), Positives = 185/359 (51%), Gaps = 35/359 (9%) Query: 15 NPQQDSDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTR 74 +PQ+ L + +E DG ++GPSGCGK+T+L +++GL PS G + R V R Sbjct: 41 SPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDR 100 Query: 75 ASPQERNIAQVFQFPVIYDTMTVAENLAFPLRN---------------RKVP-------- 111 + R+IA VFQ +Y ++V +NLAF LR R +P Sbjct: 101 LPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPE 160 Query: 112 -EGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQKISLGRGLVRADVAAVLFDEPLTVI 170 E +IK+RV +A ML++ L+++ L+ KQ+++LGR + R + L DEPL+ + Sbjct: 161 QEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIAR-NPQVFLMDEPLSNL 219 Query: 171 DPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALTFADQVVVMTRGKAVQVGSADALFER 230 D L+ + R ++ + +L +T +YVTHDQ EA+T D++ V+ RG QV S +++R Sbjct: 220 DAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDR 279 Query: 231 PAHTFVGHFIGSPGMNFLPA------HRDGENLSVAGHRLASPVGRALPAGALQVGIRPE 284 PA+ FV FIGSP MN +P EN PV R +++GIRPE Sbjct: 280 PANRFVAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPE 339 Query: 285 YLALAQPQQAGALPGTVVQVQDIGTYQMLTAKVGEH--TVKARFTPETRLPSSGDTAWL 341 +L + L TV V+ +G+ + ++ E V+AR P+ + GD WL Sbjct: 340 HLEVGAAASKNLLI-TVTGVEALGSDTFIAGELKESGIAVQARLAPQ-QCWQMGDRLWL 396 Lambda K H 0.320 0.136 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 361 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 417 Length adjustment: 30 Effective length of query: 328 Effective length of database: 387 Effective search space: 126936 Effective search space used: 126936 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory